Exploring bat-inspired cyclic tryptophan diketopiperazines as ABCB1 Inhibitors

Chemotherapy-induced drug resistance remains a major cause of cancer recurrence and patient mortality. ATP binding cassette subfamily B member 1 (ABCB1) transporter overexpression in tumors contributes to resistance, yet current ABCB1 inhibitors have been unsuccessful in clinical trials. To address this challenge, we propose a new strategy using tryptophan as a lead molecule for developing ABCB1 inhibitors. Our idea stems from our studies on bat cells, as bats have low cancer incidences and high ABCB1 expression. We hypothesized that potential ABCB1 substrates in bats could act as competitive inhibitors in humans. By molecular simulations of ABCB1-substrate interactions, we generated a benzylated Cyclo-tryptophan (C3N-Dbn-Trp2) that inhibits ABCB1 activity with efficacy comparable to or better than the classical inhibitor, verapamil. C3N-Dbn-Trp2 restored chemotherapy sensitivity in drug-resistant human cancer cells with no adverse effect on cell proliferation. Our unique approach presents a promising lead toward developing effective ABCB1 inhibitors to treat drug-resistant cancers.


REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author): The authors have effectively addressed the comments raised previously.The revised version is substantially improved.Review of comments raised by reviewer 3: Comment 1: The authors satisfactorily addressed the comments by adding relevant changes to the revised manuscript.The authors should cite a ref for (Lastly, the failure of clinical trials for ABCB1 inhibitors can be attributed to several factors, 487 including alternative cellular detoxification pathways) in Lines 486-489.
Comment 2: This was addressed by providing a snapshot structure-based design approach using cryo-EM structures of relevant transporters.Also, given information as to utility of this approach to design new ABCB1 inhibitors.No further comments on this.
Comment 3: The authors have now included more physiological environment while simulating ABCB1 and their cyclo inhibitor.Thus, the quality of computational predictions has enhanced compared to the previously used less physiological environment.I also agree that computational predictions should always be concluded with caution, which the authors have attempted.Also, I like the cautionary note now added in lines 232-236.Docking comment: The authors have answered this comment by performing simulations by using suggested PDB structures and concluded that their original choice gave the best results that aligns with their experimental observations.Comment 4: in vivo study not needed for this exploratory study wherein lead compound still need refinement before it can be suitable for animal studies.The authors have now included known P-gp inhibitor, tariquidar, as a positive control.
Comment 5: The authors have optical rotation (Suppl.compound details) as proof to demonstrate enantiomeric purity.

Reviewer #1 (Remarks to the Author):
The authors have effectively addressed the comments raised previously.The revised version is substantially improved.
We appreciate the reviewer for taking the time to thoroughly review our manuscript.

Review of comments raised by reviewer 3:
Comment 1: The authors satisfactorily addressed the comments by adding relevant changes to the revised manuscript.
The authors should cite a ref for (Lastly, the failure of clinical trials for ABCB1 inhibitors can be attributed to several factors, 487 including alternative cellular detoxification pathways) in Lines 486-489.
We thank the reviewer for the suggestion to include the reference.Accordingly, we included the reference.
Comment 2: This was addressed by providing a snapshot structure-based design approach using cryo-EM structures of relevant transporters.Also, given information as to utility of this approach to design new ABCB1 inhibitors.
No further comments on this.
We appreciate the reviewer's positive assessment of this point.
Comment 3: The authors have now included more physiological environment while simulating ABCB1 and their cyclo inhibitor.Thus, the quality of computational predictions has enhanced compared to the previously used less physiological environment.I also agree that computational predictions should always be concluded with caution, which the authors have attempted.Also, I like the cautionary note now added in lines 232-236.Docking comment: The authors have answered this comment by performing simulations by using suggested PDB structures and concluded that their original choice gave the best results that aligns with their experimental observations.We are grateful for the reviewer's acknowledgment of the improvement and strengths of this section.
Comment 4: in vivo study not needed for this exploratory study wherein lead compound still need refinement before it can be suitable for animal studies.The authors have now included known P-gp inhibitor, tariquidar, as a positive control.
We thank the reviewer for their understanding regarding the exclusion of in vivo studies at this early stage of lead compound development.
Comment 5: The authors have optical rotation (Suppl.compound details) as proof to demonstrate enantiomeric purity.
We thank the reviewer for the favorable comments regarding this aspect of the manuscript.